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MCL coexpression mm9:362: Difference between revisions

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{{MCL_coexpression_mm9
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density;0.00256092968317102;14799,14812!GO:0007613;memory;0.00256092968317102;14799,14812!GO:0005234;extracellular-glutamate-gated ion channel activity;0.00256092968317102;14799,14812!GO:0004970;ionotropic glutamate receptor activity;0.00256092968317102;14799,14812!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0104762422911387;14799,14812!GO:0008066;glutamate receptor activity;0.0104762422911387;14799,14812!GO:0022836;gated channel activity;0.0111973697202879;67516,14799,14812!GO:0017047;adrenocorticotropin-releasing hormone binding;0.014207378685594;12919!GO:0005230;extracellular ligand-gated ion channel activity;0.014207378685594;14799,14812!GO:0007611;learning and/or memory;0.014207378685594;14799,14812!GO:0005216;ion channel activity;0.014207378685594;67516,14799,14812!GO:0022838;substrate specific channel activity;0.014207378685594;67516,14799,14812!GO:0015276;ligand-gated ion channel activity;0.014207378685594;14799,14812!GO:0022834;ligand-gated channel activity;0.014207378685594;14799,14812!GO:0022803;passive transmembrane transporter activity;0.014207378685594;67516,14799,14812!GO:0015267;channel activity;0.014207378685594;67516,14799,14812!GO:0017046;peptide hormone binding;0.0160449762951106;12919!GO:0005624;membrane fraction;0.0185930011660257;12891,14799,14812!GO:0045211;postsynaptic membrane;0.0185930011660257;14799,14812!GO:0007616;long-term memory;0.0185930011660257;14799!GO:0001786;phosphatidylserine binding;0.0185930011660257;12891!GO:0050966;detection of mechanical stimulus during sensory perception of pain;0.0185930011660257;14812!GO:0044456;synapse part;0.0205067839558832;14799,14812!GO:0000267;cell fraction;0.0215318161976552;12891,14799,14812!GO:0031623;receptor internalization;0.0218104098803347;14799!GO:0017146;N-methyl-D-aspartate selective glutamate receptor complex;0.0252373070572831;14812!GO:0048266;behavioral response to pain;0.0252373070572831;14812!GO:0004972;N-methyl-D-aspartate selective glutamate receptor activity;0.0291959709185147;14812!GO:0001967;suckling behavior;0.0314401883232241;14812!GO:0042562;hormone binding;0.0314401883232241;12919!GO:0015075;ion transmembrane transporter activity;0.0314401883232241;67516,14799,14812!GO:0060079;regulation of excitatory postsynaptic membrane potential;0.0330135045063673;14812!GO:0035254;glutamate receptor binding;0.0330135045063673;14812!GO:0045471;response to ethanol;0.0358193650359458;14812!GO:0006811;ion transport;0.0358193650359458;67516,14799,14812!GO:0008328;ionotropic glutamate receptor complex;0.0358193650359458;14812!GO:0001662;behavioral fear response;0.0358193650359458;14812!GO:0002209;behavioral defense response;0.0358193650359458;14812!GO:0022891;substrate-specific transmembrane transporter activity;0.0371035929292651;67516,14799,14812!GO:0050974;detection of mechanical stimulus during sensory perception;0.0371035929292651;14812!GO:0048265;response to pain;0.0371035929292651;14812!GO:0060078;regulation of postsynaptic membrane potential;0.0371035929292651;14812!GO:0001964;startle response;0.0371035929292651;14812!GO:0042734;presynaptic membrane;0.0371035929292651;14812!GO:0050982;detection of mechanical stimulus;0.0392926393149871;14812!GO:0005261;cation channel activity;0.0396606778395125;67516,14812!GO:0005003;ephrin receptor activity;0.0396606778395125;13840!GO:0048168;regulation of neuronal synaptic plasticity;0.0396606778395125;14812!GO:0042596;fear response;0.0416161106041566;14812!GO:0006898;receptor-mediated endocytosis;0.0427397751399025;14799!GO:0022857;transmembrane transporter activity;0.0427397751399025;67516,14799,14812!GO:0009612;response to mechanical stimulus;0.0435838236247918;14812!GO:0051899;membrane depolarization;0.0435838236247918;14812!GO:0005856;cytoskeleton;0.0448179055878803;545156,14799,14812!GO:0046873;metal ion transmembrane transporter 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|gostat_on_MCL_coexpression=GO:0014069;postsynaptic density;0.00256092968317102;14799,14812!GO:0007613;memory;0.00256092968317102;14799,14812!GO:0005234;extracellular-glutamate-gated ion channel activity;0.00256092968317102;14799,14812!GO:0004970;ionotropic glutamate receptor activity;0.00256092968317102;14799,14812!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0104762422911387;14799,14812!GO:0008066;glutamate receptor activity;0.0104762422911387;14799,14812!GO:0022836;gated channel activity;0.0111973697202879;67516,14799,14812!GO:0017047;adrenocorticotropin-releasing hormone binding;0.014207378685594;12919!GO:0005230;extracellular ligand-gated ion channel activity;0.014207378685594;14799,14812!GO:0007611;learning and/or memory;0.014207378685594;14799,14812!GO:0005216;ion channel activity;0.014207378685594;67516,14799,14812!GO:0022838;substrate specific channel activity;0.014207378685594;67516,14799,14812!GO:0015276;ligand-gated ion channel activity;0.014207378685594;14799,14812!GO:0022834;ligand-gated channel activity;0.014207378685594;14799,14812!GO:0022803;passive transmembrane transporter activity;0.014207378685594;67516,14799,14812!GO:0015267;channel activity;0.014207378685594;67516,14799,14812!GO:0017046;peptide hormone binding;0.0160449762951106;12919!GO:0005624;membrane fraction;0.0185930011660257;12891,14799,14812!GO:0045211;postsynaptic membrane;0.0185930011660257;14799,14812!GO:0007616;long-term memory;0.0185930011660257;14799!GO:0001786;phosphatidylserine binding;0.0185930011660257;12891!GO:0050966;detection of mechanical stimulus during sensory perception of pain;0.0185930011660257;14812!GO:0044456;synapse part;0.0205067839558832;14799,14812!GO:0000267;cell fraction;0.0215318161976552;12891,14799,14812!GO:0031623;receptor internalization;0.0218104098803347;14799!GO:0017146;N-methyl-D-aspartate selective glutamate receptor complex;0.0252373070572831;14812!GO:0048266;behavioral response to pain;0.0252373070572831;14812!GO:0004972;N-methyl-D-aspartate selective glutamate receptor activity;0.0291959709185147;14812!GO:0001967;suckling behavior;0.0314401883232241;14812!GO:0042562;hormone binding;0.0314401883232241;12919!GO:0015075;ion transmembrane transporter activity;0.0314401883232241;67516,14799,14812!GO:0060079;regulation of excitatory postsynaptic membrane potential;0.0330135045063673;14812!GO:0035254;glutamate receptor binding;0.0330135045063673;14812!GO:0045471;response to ethanol;0.0358193650359458;14812!GO:0006811;ion transport;0.0358193650359458;67516,14799,14812!GO:0008328;ionotropic glutamate receptor complex;0.0358193650359458;14812!GO:0001662;behavioral fear response;0.0358193650359458;14812!GO:0002209;behavioral defense response;0.0358193650359458;14812!GO:0022891;substrate-specific transmembrane transporter activity;0.0371035929292651;67516,14799,14812!GO:0050974;detection of mechanical stimulus during sensory perception;0.0371035929292651;14812!GO:0048265;response to pain;0.0371035929292651;14812!GO:0060078;regulation of postsynaptic membrane potential;0.0371035929292651;14812!GO:0001964;startle response;0.0371035929292651;14812!GO:0042734;presynaptic membrane;0.0371035929292651;14812!GO:0050982;detection of mechanical stimulus;0.0392926393149871;14812!GO:0005261;cation channel activity;0.0396606778395125;67516,14812!GO:0005003;ephrin receptor activity;0.0396606778395125;13840!GO:0048168;regulation of neuronal synaptic plasticity;0.0396606778395125;14812!GO:0042596;fear response;0.0416161106041566;14812!GO:0006898;receptor-mediated endocytosis;0.0427397751399025;14799!GO:0022857;transmembrane transporter activity;0.0427397751399025;67516,14799,14812!GO:0009612;response to mechanical stimulus;0.0435838236247918;14812!GO:0051899;membrane depolarization;0.0435838236247918;14812!GO:0005856;cytoskeleton;0.0448179055878803;545156,14799,14812!GO:0046873;metal ion transmembrane transporter activity;0.0449524136953147;67516,14812!
|ontology_enrichment_celltype=CL:0000117!6.53e-13!23;CL:0000337!6.53e-13!23;CL:0000540!3.45e-08!33;CL:0000047!3.45e-08!33;CL:0000031!3.45e-08!33;CL:0000404!3.45e-08!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.03e-30!54;UBERON:0002346!2.33e-28!64;UBERON:0003075!2.33e-28!64;UBERON:0007284!2.33e-28!64;UBERON:0001049!2.74e-28!52;UBERON:0005068!2.74e-28!52;UBERON:0006241!2.74e-28!52;UBERON:0007135!2.74e-28!52;UBERON:0002020!6.33e-26!34;UBERON:0001017!3.52e-24!73;UBERON:0010371!4.10e-24!73;UBERON:0000955!1.69e-23!47;UBERON:0006238!1.69e-23!47;UBERON:0001016!3.93e-23!75;UBERON:0002616!2.61e-22!46;UBERON:0003056!4.28e-22!49;UBERON:0004121!5.75e-21!95;UBERON:0000924!5.75e-21!95;UBERON:0006601!5.75e-21!95;UBERON:0003528!7.03e-21!29;UBERON:0002791!7.03e-21!29;UBERON:0001893!7.03e-21!29;UBERON:0003080!4.65e-20!40;UBERON:0002780!5.09e-19!39;UBERON:0001890!5.09e-19!39;UBERON:0006240!5.09e-19!39;UBERON:0010314!4.42e-16!92;UBERON:0000956!1.98e-15!21;UBERON:0001869!1.98e-15!21;UBERON:0000203!1.98e-15!21;UBERON:0002021!3.65e-13!10;UBERON:0000411!3.65e-13!10;UBERON:0001950!3.65e-13!10;UBERON:0002619!6.09e-13!17;UBERON:0003076!1.05e-08!12;UBERON:0003057!1.05e-08!12;UBERON:0002240!2.67e-07!6;UBERON:0005174!2.67e-07!6;UBERON:0001137!2.67e-07!6
}}

Latest revision as of 15:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:106069742..106069754,+p@chr10:106069742..106069754
+
Mm9::chr11:56825300..56825329,+p1@Gria1
Mm9::chr11:56825334..56825345,+p3@Gria1
Mm9::chr11:56825447..56825448,+p10@Gria1
Mm9::chr13:96214655..96214666,-p2@Crhbp
Mm9::chr14:56129430..56129468,+p1@Cpne6
Mm9::chr14:76362222..76362254,+p@chr14:76362222..76362254
+
Mm9::chr14:76362263..76362291,+p@chr14:76362263..76362291
+
Mm9::chr14:88870750..88870829,-p@chr14:88870750..88870829
-
Mm9::chr16:34514130..34514142,-p17@Kalrn
Mm9::chr16:34514149..34514165,-p11@Kalrn
Mm9::chr16:34514170..34514214,-p3@Kalrn
Mm9::chr16:34514261..34514270,-p19@Kalrn
Mm9::chr16:34514291..34514297,-p27@Kalrn
Mm9::chr16:60605097..60605117,-p1@Epha6
Mm9::chr16:60605371..60605385,-p3@Epha6
Mm9::chr16:60605417..60605435,-p4@Epha6
Mm9::chr16:7217845..7217853,+p33@Rbfox1
Mm9::chr18:86564394..86564405,+p5@Neto1
Mm9::chr6:136123290..136123321,-p@chr6:136123290..136123321
-
Mm9::chr7:98691574..98691605,+p17@Dlg2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0014069postsynaptic density0.00256092968317102
GO:0007613memory0.00256092968317102
GO:0005234extracellular-glutamate-gated ion channel activity0.00256092968317102
GO:0004970ionotropic glutamate receptor activity0.00256092968317102
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0104762422911387
GO:0008066glutamate receptor activity0.0104762422911387
GO:0022836gated channel activity0.0111973697202879
GO:0017047adrenocorticotropin-releasing hormone binding0.014207378685594
GO:0005230extracellular ligand-gated ion channel activity0.014207378685594
GO:0007611learning and/or memory0.014207378685594
GO:0005216ion channel activity0.014207378685594
GO:0022838substrate specific channel activity0.014207378685594
GO:0015276ligand-gated ion channel activity0.014207378685594
GO:0022834ligand-gated channel activity0.014207378685594
GO:0022803passive transmembrane transporter activity0.014207378685594
GO:0015267channel activity0.014207378685594
GO:0017046peptide hormone binding0.0160449762951106
GO:0005624membrane fraction0.0185930011660257
GO:0045211postsynaptic membrane0.0185930011660257
GO:0007616long-term memory0.0185930011660257
GO:0001786phosphatidylserine binding0.0185930011660257
GO:0050966detection of mechanical stimulus during sensory perception of pain0.0185930011660257
GO:0044456synapse part0.0205067839558832
GO:0000267cell fraction0.0215318161976552
GO:0031623receptor internalization0.0218104098803347
GO:0017146N-methyl-D-aspartate selective glutamate receptor complex0.0252373070572831
GO:0048266behavioral response to pain0.0252373070572831
GO:0004972N-methyl-D-aspartate selective glutamate receptor activity0.0291959709185147
GO:0001967suckling behavior0.0314401883232241
GO:0042562hormone binding0.0314401883232241
GO:0015075ion transmembrane transporter activity0.0314401883232241
GO:0060079regulation of excitatory postsynaptic membrane potential0.0330135045063673
GO:0035254glutamate receptor binding0.0330135045063673
GO:0045471response to ethanol0.0358193650359458
GO:0006811ion transport0.0358193650359458
GO:0008328ionotropic glutamate receptor complex0.0358193650359458
GO:0001662behavioral fear response0.0358193650359458
GO:0002209behavioral defense response0.0358193650359458
GO:0022891substrate-specific transmembrane transporter activity0.0371035929292651
GO:0050974detection of mechanical stimulus during sensory perception0.0371035929292651
GO:0048265response to pain0.0371035929292651
GO:0060078regulation of postsynaptic membrane potential0.0371035929292651
GO:0001964startle response0.0371035929292651
GO:0042734presynaptic membrane0.0371035929292651
GO:0050982detection of mechanical stimulus0.0392926393149871
GO:0005261cation channel activity0.0396606778395125
GO:0005003ephrin receptor activity0.0396606778395125
GO:0048168regulation of neuronal synaptic plasticity0.0396606778395125
GO:0042596fear response0.0416161106041566
GO:0006898receptor-mediated endocytosis0.0427397751399025
GO:0022857transmembrane transporter activity0.0427397751399025
GO:0009612response to mechanical stimulus0.0435838236247918
GO:0051899membrane depolarization0.0435838236247918
GO:0005856cytoskeleton0.0448179055878803
GO:0046873metal ion transmembrane transporter activity0.0449524136953147



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)6.53e-1323
neuroblast (sensu Vertebrata)6.53e-1323
neuron3.45e-0833
neuronal stem cell3.45e-0833
neuroblast3.45e-0833
electrically signaling cell3.45e-0833

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.03e-3054
neurectoderm2.33e-2864
neural plate2.33e-2864
presumptive neural plate2.33e-2864
neural tube2.74e-2852
neural rod2.74e-2852
future spinal cord2.74e-2852
neural keel2.74e-2852
gray matter6.33e-2634
central nervous system3.52e-2473
ecto-epithelium4.10e-2473
brain1.69e-2347
future brain1.69e-2347
nervous system3.93e-2375
regional part of brain2.61e-2246
pre-chordal neural plate4.28e-2249
ectoderm-derived structure5.75e-2195
ectoderm5.75e-2195
presumptive ectoderm5.75e-2195
brain grey matter7.03e-2129
regional part of telencephalon7.03e-2129
telencephalon7.03e-2129
anterior neural tube4.65e-2040
regional part of forebrain5.09e-1939
forebrain5.09e-1939
future forebrain5.09e-1939
structure with developmental contribution from neural crest4.42e-1692
cerebral cortex1.98e-1521
cerebral hemisphere1.98e-1521
pallium1.98e-1521
occipital lobe3.65e-1310
visual cortex3.65e-1310
neocortex3.65e-1310
regional part of cerebral cortex6.09e-1317
posterior neural tube1.05e-0812
chordal neural plate1.05e-0812
spinal cord2.67e-076
dorsal region element2.67e-076
dorsum2.67e-076


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.00933497
MA0004.10.15514
MA0006.10.486909
MA0007.11.41117
MA0009.10.499857
MA0014.10.0202604
MA0017.10.074682
MA0019.10.344318
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.10.067163
MA0029.10.442582
MA0030.10.448261
MA0031.10.417663
MA0038.10.256813
MA0040.10.510947
MA0041.10.109446
MA0042.10.102161
MA0043.10.586618
MA0046.10.531807
MA0048.10.638726
MA0050.10.533529
MA0051.10.263603
MA0052.10.518112
MA0055.10.358275
MA0056.10
MA0057.13.26419
MA0058.10.0984787
MA0059.10.105184
MA0060.10.0321237
MA0061.10.0422754
MA0063.10
MA0066.10.248543
MA0067.10.817149
MA0068.10.100153
MA0069.11.2887
MA0070.10.509795
MA0071.10.180178
MA0072.10.502282
MA0073.16.78556
MA0074.10.222108
MA0076.10.0840393
MA0077.10.48317
MA0078.10.289095
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.12.13087
MA0089.10
MA0090.10.416778
MA0091.10.491727
MA0092.10.826612
MA0093.10.0709755
MA0095.10
MA0098.10
MA0100.10.213782
MA0101.10.110172
MA0103.10.0799057
MA0105.10.063741
MA0106.10.295186
MA0107.10.0769078
MA0108.20.363107
MA0109.10
MA0111.10.863236
MA0113.11.37626
MA0114.10.0414319
MA0115.10.589161
MA0116.10.839093
MA0117.10.559943
MA0119.10.110503
MA0122.10.577888
MA0124.10.766819
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.236653
MA0139.10.0996617
MA0140.10.2137
MA0141.10.0898383
MA0142.10.40532
MA0143.10.285913
MA0144.10.666779
MA0145.10.0580487
MA0146.10.000787799
MA0147.10.0471319
MA0148.10.165681
MA0149.16.33911
MA0062.20.0144279
MA0035.20.217072
MA0039.20.0108975
MA0138.20.334152
MA0002.20.0238548
MA0137.20.0883456
MA0104.20.0278464
MA0047.20.256234
MA0112.20.134174
MA0065.20.134947
MA0150.10.145553
MA0151.10
MA0152.10.256315
MA0153.10.635107
MA0154.13.4293
MA0155.10.0735373
MA0156.10.0836044
MA0157.10.378326
MA0158.10
MA0159.10.423802
MA0160.10.968677
MA0161.10
MA0162.11.46529
MA0163.10.00467197
MA0164.10.23692
MA0080.20.0773362
MA0018.20.244112
MA0099.20.329046
MA0079.21.79817
MA0102.21.18455
MA0258.11.8377
MA0259.10.165891
MA0442.10
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